Genomic sequencing is an effective tool to discover the genetic basis of Mendelian disorders. Analysis of genomic sequences has revealed the existence of copy number variants (CNVs) (e.g., the number of copies of a particular gene in the genotype of an individual). CNVs may have important roles in human disease and/or drug response. However, calling CNVs from genomic sequence data (e.g., exome sequence data) is challenging. Current solutions detect CNVs from human sequencing read depth, but are not been welt-suited for large population studies on the order of tens or hundreds of thousands of exomes. Their limitations, among others, include being difficult to integrate into automated variant calling pipelines and being ill-suited for detecting common variants. These and other shortcomings are addressed in the present disclosure.